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.. -*- mode: rst; fill-column: 78 -*-
.. ex: set sts=4 ts=4 sw=4 et tw=79:
.. _faq:
**************************
Frequently Asked Questions
**************************
.. raw:: html
<div class="expandinstructions">Click on an item to expand it</div>
.. container:: foldup
Why NeuroDebian?
In the course of our own research endeavors |we| have joined forces to
develop `PyMVPA -- a Python framework for multivariate pattern analysis of
neural data <http://www.pymvpa.org>`_. To conveniently deploy PyMVPA for
anyone using Debian-derived distributions this package repository was created
initially. Besides the PyMVPA_ project |we| collaborate with the `NiPy team
<http://neuroimaging.scipy.org>`_ on various projects, such as NiBabel_ and
NiPype_. Quickly NeuroDebian_ became the ultimate integrated environment for
all these projects -- and we are constantly working on enriching this
environment with as many additional relevant software as possible.
Debian, Debian, Debian -- What about Ubuntu?
NeuroDebian offers backported binary packages for recent Ubuntu releases
whenever possible. However, since Ubuntu (like many other derivatives) uses
Debian as its foundation, it is more efficient to spend time maintaining
packages in Debian, instead of having to directly contribute to countless
child-distributions. After the appearance of new packages in Debian, Ubuntu
typically synchronizes them quickly and they become available in the *Ubuntu
universe* -- a repository of Debian packages rebuilt for a particular Ubuntu
release. We are not constantly rebuilding of all available NeuroDebian
packages for new Ubuntu releases. Therefore, you might find some packages
temporarily being available for older Ubuntu releases only -- until the point
when a new package version is made and gets built for all currently supported
releases.
How do I get a new neuroscience-related FOSS into (Neuro)Debian?
The goal of NeuroDebian is to package neuroscience software for Debian. Hence
getting software into NeuroDebian means trying to get it into Debian. There are
at least two possibilities to achieve that:
* You can approach packaging it yourself. Start by filing an ITP_ (Intent to
Package) bugreport and, if you are not a Debian developer, `ask us
<team@neuro.debian.net>`_ to mentor your upload to Debian_.
* `Contact us <team@neuro.debian.net>`_ and we'll do the work for you, but
then it might take a little longer, depending on our current workload and
interest in a particular software.
I have heard that some packages are non-free. Will you charge me for them?
No. The term :term:`non-free` refers to an archive section. NeuroDebian uses
exactly the same `archive sections as Debian proper
<http://www.debian.org/doc/debian-policy/ch-archive.html>`_. The *non-free*
section contains packages that have certain restrictions regarding **your
freedom** to employ them for a particular purpose. In contrast, for packages
in the *main* section your are completely free to do whatever and in whatever
context you like. Regardless of the actual license or archive section, all
packages in NeuroDebian are provided free of charge and under the licensing
terms of the original developers.
When does a package migrate from NeuroDebian into Debian proper?
In short: When it is ready. The longer answer is that there is nothing
special to packages in NeuroDebian in comparison to packages conducted
elsewhere. Packaging efforts are announced to Debian via ITPs_ and the
packaging itself is available in some version control system -- typically in
the Git repositories of the `pkg-exppsy group on Debian's Alioth server`_, or
another VCS, or on http://mentors.debian.net.
The only difference is that a particular package becomes available through the
NeuroDebian repository before it has passed all checks for compliance with
Debian's standards. But even after a package becomes part of Debian, the
NeuroDebian repository continues to provide binary packages of new versions
for a recent set of Debian and Ubuntu releases (aka backports).
.. _pkg-exppsy group on Debian's Alioth server: http://alioth.debian.org/projects/pkg-exppsy/
How to create a mirror of the repository?
The NeuroDebian repository can be mirrored with rsync. If you are interested
in sponsoring storage space and bandwidth for another mirror, please
`contact us <team@neuro.debian.net>`_.
.. _sec_pkg_authentication:
What means "The following signatures couldn't be verified..."?
When you start using this repository, you probably get warning messages
like this::
The following signatures couldn't be verified because
the public key is not available.
Or you will be asked questions like this over and over::
WARNING: The following packages cannot be authenticated!
...
Install these packages without verification [y/N]?
This is because your APT installation initially does not know the GPG
key that is used to sign the release files of this repository. It is easy to
make APT happy again. The simplest way is to install the ``neurodebian-archive-keyring``
package that is available from the NeuroDebian repository. Alternatively:
1. Get the key. Either download the `repository key from here
<_static/neuro.debian.net.asc>`_
or fetch it from http://wwwkeys.pgp.net (0x439754ED1F42AA2C).
2. On modern Debian and Ubuntu systems with `/etc/apt/trusted.gpg.d/` just install that key under that folder, e.g.::
wget -q -O/etc/apt/trusted.gpg.d/neuro.debian.net.asc https://neuro.debian.net/_static/neuro.debian.net.asc
On older systems with apt-key feed the key into APT by invoking::
apt-key add #file#
Where `#file#` has to be replaced with the location of the key file you just
downloaded. You need to have superuser-privileges to do this (either do it
as root or use sudo).
Why is NeuroDebian not a Pure Blend?
This is in the works, but...
There is no need for it to become one, as the existing Debian Pure Blends
already offer the desired functionality *within* Debian. Similar to Pure
Blends, NeuroDebian's goal is to provide software for neuroscientists using
the Debian operating system, and therefore the ultimate goal is to get all
relevant software **into Debian**.
However, various reasons exist that prevent a particular software from
entering Debian. Some are temporary, i.e. a package is already useable, but
some technical bits do not meet Debian's standards (yet) or a licensing issue
needs to be resolved first. For some software the licensing is so restrictive
that it cannot be distributed by Debian, and hence cannot even go into its
*non-free* branch. Unfortunately, sometimes these issues cannot be solved to
a degree that is acceptable for Debian. For some other packages Debian itself
is not ready yet, e.g. huge data packages with neuroscience data (:ref:`with
sometimes over 1GB <pkg_fsl-first-data>`).
NeuroDebian aims to be a platform that provides a staging area for
neuroscience software packages on their way into Debian. All packages are
properly registered in the relevant `Debian Pure Blends`_, e.g.
`Debian Science Cognitive Neuroscience`_ or `Debian Med Imaging`_. Inside
Debian these efforts already provide a suitable framework for this purpose,
and hence there is no need to establish yet another one.
.. _Debian Pure Blends: http://wiki.debian.org/DebianPureBlends
.. _Debian Science Cognitive Neuroscience: http://blends.alioth.debian.org/science/tasks/neuroscience-cognitive
.. _Debian Med Imaging: http://debian-med.alioth.debian.org/tasks/imaging
I want to help. How do I get involved?
We always need people to help maintaining existing packages. If you need
some additional software packaged and you want to try it on your own, we would
be happy to mentor you. We also have a :ref:`list of ongoing and planned
projects <projects>`, each listing a number of tasks that need to be done.
If you found something you are interested in, please email the
neurodebian-devel_ mailing list and let us know about it. Thanks!
How can I cite NeuroDebian?
Please cite the following paper:
Halchenko, Y. O. & Hanke, M. (2012). `Open is not enough. Let’s take the
next step: An integrated, community-driven computing platform for neuroscience
<http://www.frontiersin.org/Neuroinformatics/10.3389/fninf.2012.00022/full>`_.
*Frontiers in Neuroinformatics*, 6:22.
.. include:: link_names.txt
.. include:: substitutions.txt
|
